Correction: Oniciuc, E. A.; et al. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes 2018, 9, 268.

The authors wish to make the following changes to their paper [1]. Due to an undetected mistake in the references management, certain errors appeared in the reference list and a reference was duplicated in Table 1[...].


Reference [66] in
All sequenced isolates harbored three AMR genes against beta-lactam antibiotics encoded on the chromosome. Some isolates also harbored several other plasmid encoded resistance genes against trimethoprim, sulphonamide, and aminoglycoside antibiotics.
Mutations in housekeeping genes (gyrA at position 86, 23S rRNA at position 2074 and 2075) associated with AMR phenotypes were also identified.

Pigs
High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Correlation between MLST type and resistance profiles was only observed in S. enterica serovar Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates. To improve the concordance between genotypic and phenotypic data, it was proposed to reduce the phenotypic cut-off values for streptomycin to ≥32 µg mL −1 for both Salmonella and E. coli. [50] Helicobacter pullorum 4 Chicken meat AMR-associated SNPs were detected (linked to resistance to fluoroquinolones, macrolides, and tetracyclines).
[51] H. pullorum 11 Broiler and free-range chicken WGS revealed the presence of five or six well characterized AMR genes, including those encoding a resistance-nodulation-division efflux pump Klebsiella pneumoniae 7 Pig and human samples at abbatoirs AMR genes associated with resistance to β-lactams, aminoglycosides, fluoroquinolones, macrolides, lincosamide, streptogramins, rifampicin, sulfonamides, trimethoprim, phenicols, and tetracycline were identified. Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%).
[33] S. enterica 90 Dairy cattle and humans Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2.
[57] S. enterica serovar Typhimurium 984 Swine Multiple genotypic resistance determinants were predominant, including resistance against ampicillin, streptomycin, sulfonamides, and tetracyclines. Phenotypic resistance to enrofloxacin and ceftiofur was found in conjunction with the presence of plasmid-mediated AMR genes.
[59] S. enterica serovar Heidelberg 113 Humans, abbatoir poultry and retail poultry CMY-2 plasmids, all belonging to incompatibility group I1, were identified in cefoxitin-resistant isolates. Analysis of IncI1 plasmid sequences revealed high identity (95% to 99%) to a previously described plasmid (pCVM29188_101) found in S. enterica serovar Kentucky. The non-clinical use of narrow-spectrum penicillins (e.g., benzylpenicillin) might have favored the diffusion of plasmids carrying the bla TEM-1 gene in S. enterica serotype Typhimurium in the late 1950s.
[66] S. enterica serovar Weltevreden 44 Human stool and contaminated food samples AMR genes were only identified in eight isolates, linked to resistance to tetracycline, ciprofloxacin or ampicillin. [67] Staphylococcus aureus 66 Retail meats Eleven spa types were represented. The majority of MRSA (84.8%) possessed SCCmec IV.
[69] S. aureus 12 Livestock animals Most isolates harbored resistance genes to ≥3 antimicrobial classes in addition to β-lactams. Heavy metal resistance genes were detected in most European ccrC positive isolates, with >80% harboring czrC, encoding zinc and cadmium resistance.